From the organizers:

Dear CASP7 participants,

By now, we are one month into the CASP7 prediction season. Forty three
targets have been released during this period of time. That's already
the number of targets that were released in CASP3 or CASP4, and
approximately half of the number of targets that were released in CASP6.
If we can maintain the current flow rate of targets for the next 6
weeks, we will be able to come close to the desired mark of 100 targets
by the end of the target release season (July 21).

Targets to expire next week:
T0293 (Mon, June 12)
T0295, T0302 (Thu, June 15)
T0300 (Fri, June 16)

"Soft" (3-week) deadlines:
T0296 (Mon, June 12)
T0297, T0298 (Tue, June 13)
T0299 (Wed, June 14)
T0301 (Thu, June 15)

Next week we are planning on releasing targets Monday through Thursday.

One of the targets to be released on Monday, T0326, is a quite high
sequence similarity target. We will ask our high accuracy assessor to
pay special attention to side chain accuracy in predictions for this
target. So, please do your best in refining side chains for it.
We also want to remind, that majority of targets over some high
threshold of sequence identity to a template will undergo a detailed
assessment of other features, particularly loops, functional sites,
value added over a template, etc. These targets are not specified in
advance and threshold will be determined by the high accuracy assessor.

We asked our target suppliers to extend public release date for a couple
of targets that we wanted to suggest for model refinement (we are
planning on having a few more of these by the end of the prediction
season). First of these targets, T0288, has expired for prediction
today. The experimentalists kindly provided us with the coordinates for
T0288 ahead of time. We have started preliminary evaluation of models
for this target and hopefully we will be able to determine one of the
best models for it according to the GDT_TS score over the weekend. Then
we will contact the author of this model and ask him/her for the
permission for public release of the model. Then the model for the
refinement will be posted at our web site and you will have
approximately 3 more weeks to submit your refinement results as regular
TS models with one adjustment - target name will need to be specified as
TR288 (letter "R" instead of "0" in the target name). We will send you a
reminder when the appropriate model is selected for refinement (likely
early next week).

CASP6 participants might remember that in the previous round of our
experiment we asked predictors to submit multi-chain models for a target
that was specified by the the experimentalists as oligomeric. Last time
we got a very sparse response in this category and therefore, results
were not assessed. We decided to give another try to this initiative
this round of CASP. Target T0300 was specified by its supplier as a
dimer. This target is to expire in a week on June 16. Please, start
working on the dimeric model for this target if you plan to submit it
(obviously, this option is in ADDITION, not alternative, to the usual
CASP one-chain prediction).
Format requirements:
1. Only TS-type predictions will be accepted for oligomers.
2. Target record should be in the form
TARGET T0300 OLIGOMER
3. Each monomer should be identified as a separate chain, consecutive
capital letters for chain IDs should be used (in this case A and B).
4. Residue numbering in each chain starts from 1.
5. No TER or END records between monomers (chains).
Please, note that we are currently working on implementing details of
this format in our format verificators, so you won't be able to submit
oligomeric prediction over the weekend. We hope to have our system ready
for accepting this kind of predictions on Monday.


--
Andriy Kryshtafovych,
for CASP organizers

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This "transparency", this immediate sharing of purpose and status is one of the things that, IMHO, increases the loyalty of those donating CPU cycles to this project.

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Rosie, Rosie, she's our gal,
If she can't do it, no one shall!

How exciting! T288 was a relatively small target with only 93 amino acids. I remeber crunching some t288-WUs. Now cross your fingers that Rosetta has provided the best model for it!

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Targets to expire next week:
T0293 (Mon, June 12)
T0295, T0302 (Thu, June 15)
T0300 (Fri, June 16)

I would, however, gently suggest that we not abort any of these units until we receive an official word from someone at David's Lab to do so.

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E-Mail from the CASP team 14/6/2006

T0295 - forcing "soft" deadline.
It is always a pity when a target gets exposed ahead of time. This time
this happened to T0295. The target was to be closed tomorrow but we were
forced to close accepting predictions for it today because of the early
PDB release (2ihr). In this case the 3-week rule is used. All the
predictions that reached us within the 3-week period since the target
release will be evaluated. All the models accepted after June 12 will be
canceled (even if you received the message that the prediction has been
accepted, but this happened on or after June 13). Fortunately, many of
you took our "soft" deadlines seriously and did submit predictions on
this target before its "soft" deadline.

4 targets have been released by the PDB.
Besides T0295, three other CASP structures have been released by the PDB
this week T0290, T0291 and T0293 (see our target list page). So, you may
check now how well you did on these targets.

T0288 - refinement.
We have finished preliminary automatic evaluation of 3D predictions
submitted on T0288. Analysing results, we were "disappointed" to learn
that initial modeling went very well leaving not much room for the
refinement. Nevertheless, we want to proceed with our initial intention
and do suggest one of the best models for this target for refinement.
This task is pretty challenging but we can see that there are some
details in the prediction that can be improved. The model selected for
the refinement can be found following "Refinement" link from Targets
section of the casp7 web page. Your refined models should be submitted
as regular TS predictions for the target TR288.

Target release update.
Two last targets for this week will be released tomorrow.

--
Andriy Kryshtafovych,
for CASP organizers

---

Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

E-Mail from CASP team 16/06/2006

Bad news first ...
It was brought to our attention that a paper was published on CASP7
structure T0294 ( http://dx.doi.org/10.1016/j.jmb.2006.05.018 ).
As this happened less than 3 weeks after the target release, we are
canceling this target according to our rules. No models will be assessed
on this target. This information leak is not a fault of the SG center
that provided the target, as the publication is from another group that
solved the same protein.

Multimers.
Besides T0295 and T0300 (already closed), we are accepting multi-chain
predictions for T0305, T0308, T0310 and T0332. Please check our web site
for format.

Targets to expire next week:
T0305 (Tue, June 20)
T0283, T0308 (Wed, June 21)
T0297 (Thu, June 22)
T0298, T0313 (Fri, June 23)
T0296 (Sat, June 24)


"Soft" (3-week) deadlines:
T0303, T0304 (Tue, June 20)
T0306, T0307 (Wed, June 21)
T0309 - T0311 (Thu, June 22)
T0312, T0314 (Fri, June 23)


--
Andriy Kryshtafovych,
for CASP organizers

---

Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

E-Mail from CASP team 16/06/2006

Bad news first ...
It was brought to our attention that a paper was published on CASP7
structure T0294 ( http://dx.doi.org/10.1016/j.jmb.2006.05.018 ).
As this happened less than 3 weeks after the target release, we are
canceling this target according to our rules. No models will be assessed
on this target. This information leak is not a fault of the SG center
that provided the target, as the publication is from another group that
solved the same protein.

Multimers.
Besides T0295 and T0300 (already closed), we are accepting multi-chain
predictions for T0305, T0308, T0310 and T0332. Please check our web site
for format.

Targets to expire next week:
T0305 (Tue, June 20)
T0283, T0308 (Wed, June 21)
T0297 (Thu, June 22)
T0298, T0313 (Fri, June 23)
T0296 (Sat, June 24)


"Soft" (3-week) deadlines:
T0303, T0304 (Tue, June 20)
T0306, T0307 (Wed, June 21)
T0309 - T0311 (Thu, June 22)
T0312, T0314 (Fri, June 23)


--
Andriy Kryshtafovych,
for CASP organizers

we were disappointed that T294 got cancelled, because Vatson and Bin had already put a fair amount of work into it. but fortunately it had not gotten sent out to rosetta@home, so none of you wasted cycles!

---

Do you know how well you did on T288? Was it the Rosetta model which was too close to the native structure that there was no room left for refinement? What's the first picture of the Rosettapredictions for the already published casp targets?

---

Bump.

---

dag
--Finding aliens is cool, but understanding the structure of proteins is useful.

For Casp6, we didn't find out how the projects did - until a few months after the last submission. So we probably won't find out this year, either.. until well after August. (Although it'd be nice to know ahead of that..)

---

For Casp6, we didn't find out how the projects did - until a few months after the last submission. So we probably won't find out this year, either.. until well after August. (Although it'd be nice to know ahead of that..)

Yes--this is true. all the hard work is now, and we don't find out for quite a while about how well we did for most of the targets. a few of the true structures have been released, but only for the easy homolog modeling targets, none of which used rosetta@home. so we all have to be patient for a couple of months--it isn't hard for us, as we are being swamped with new prediction targets every day!

---

Target release schedule for 2 next weeks.
We will have only 3 days of target release in the week of
July 3 (Wed-Fri). To compensate for this, we are planning
on releasing targets every weekday (Mon-Fri) next week.

Targets to expire next week:
T0285, T0286, T0310 (Mon, June 26)
T0315, T0316 (Tue, June 27)
T0317, T0320 (Wed, June 28)
T0322 (Thu, June 29)
T0299, T0323 (Fri, June 30)
T0324 (Sat, Jul 1)

"Soft" deadlines:
T0315-317 (Mon, June 26)
T0318, T0319 (Tue, June 27)
T0321, T0322 (Wed, June 28)
T0323-325 (Thu, June 29)

Multimers.
Three new multimers were released last week:
T0338, T0339 and T0343.
They are available for prediction in the oligomer format
(additionally to the usual CASP monomer prediction).
List of other targets for oligomer predictions:
T0295, T0300, T0305, T0308 (expired)
T0310 (to expire next Monday)
T0332 (to expire on Jul 8)

Side chain refinement targets.
T0326 (already announced)
T0340 (released this week)
T0345 and T0346 (to be released next Monday)

Model Refinement.
We are clarifying details of 3 more potential targets for
model refinement with the crystallographers. Next week we
will issue an announcement if any of these targets proved to
be suitabile for refinement.

--
Andriy Kryshtafovych,
for CASP organizers

---

Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

Reminding that no targets will be released next Monday and Tuesday.
We have 9 targets scheduled for release Wednesday through Friday.

An additional target has been released this week for refinement (follow
the "Refinement" link from our main CASP7 web page). The other two
candidates for refinement were rejected by organizers.

Targets to expire next week:
T0326, T0328 (Wed, July 5)
T0301, T0329 (Thu, July 6)
T0309, T0311 (Fri, July 7)
T0330, T0332 (Sat, July 8)
T0321, T0333 (Sun, July 9)

Soft deadlines:
T0326, T0327 (Mon, July 3)
T0328, T0329 (Tue, July 4)
T0330, T0331 (Wed, July 5)
T0332, T0333 (Thu, July 6)

--
Andriy Kryshtafovych,
for CASP organizers

---

Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

Dear predictors,

Target release schedule for the next 2 weeks:
We are approaching the end of CASP7 target release season
(July 21). This leaves us with 2 extra weeks to reach the
goal of ~100 targets in CASP7. We are pretty much on schedule
and plan to release enough targets next week, so that you have
at least 3 full weeks to complete predictions (having in mind
that the end of the prediction season is scheduled for August 4).
Therefore, you should be prepared to receive up to 3 targets per
day, Monday through Friday. More definite plans for the week of
July 17 will be announced in our weekly update on July 14. Please
also note that depending on the next week target supply, we may
slightly extend the end of the prediction season (2-3 days max)
in order to prevent an overload in the week of July 31 (otherwise
we would need to have 5-6 targets/day closing that week).

Warning for server groups:
We want to remind that the extra 24 hour grace period in addition
to the regular 48 hours for accepting server predictions is intended
solely to allow correcting any technical errors and not for changing
the prediction content. Our policy is to reject the prediction if
there exists an evidence that someone attempted to manipulate the
deadlines. We may make server corrections public in the future.

Side chain refinement targets.
T0326, T0340, T0345, T0346 (already announced); T0359 (released this
week), T0366 (to be released next Monday).

Targets to expire next week:
T0303, T0304 (Mon, July 10)
T0306, T0307 (Tue, July 11)
T0312, T0334 (Wed, July 12)
T0314, T0340 (Thu, July 13)
T0318, T0319 (Fri, July 14)
T0338, T0339 (Sat, July 15)
T0341, T0343 (Sun, July 16)

Soft deadlines:
T0334, T0335 (Mon, July 10)
T0338-340 (Wed, July 12)
T0341-343 (Thu, July 13)

--
Andriy Kryshtafovych,
for CASP organizers

---

Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

Dear predictors,

Today we have closed the facility for submitting targets for CASP7.
We are happy to announce that we have reached the goal of 100 targets
for prediction in CASP7. As former CASP participants remember, this had
been a goal since several CASPs.

All in all, we have received 154 submissions of which we selected 104
targets for CASP7, and as of today 98 of these have been released. This
means that we are left with 6 targets for next week. We plan to release
three targets on Monday, two on Tuesday and the last one on Wednesday.
To reduce possible overload in the last week, we are extending the
prediction season by 3 days. The deadline for the last CASP7 target will
be August 7.

At the end of the target release season we would like to thank all the
crystallographers and NMR spectroscopists who supported the experiment.
Especially big thanks go to the four structural genomic centers (JCSG,
MCSG, NESG and SGC) which provided the biggest share by submitting 20+
targets each. The full list of the people/centers submitting targets for
CASP7 will be published shortly at the CASP7 target submission page.

We also want to thank the PDB for arranging a special mechanism so that
the proteins deposited to the PDB with the "CASP" annotation were put on
hold for at least 4 weeks.

This week we had to cancel target T0377 as its structure had been
released by the PDB (2ivy). Second time this season a different
crystallography center independently solved and published the structure
submitted to CASP.

Complete list of targets (13) for oligomeric predictions:
T0295, T0300, T0305, T0308, T0310, T0332 (expired);
T0338, T0339, T0343, T0346, T0366, T0372, T0375 (valid for prediction).

Complete list of side chain refinement targets (6):
T0326, T0340, T0345, T0346, T0359, T0366

Targets for high accuracy assessment:
Not specified in advance, this will be determined by the assessors.

Targets for refinement:
TR288, TR308; additional targets are considered.

Targets to expire next week:
T0345, T0346 (Mon, July 17)
T0348, T0349 (Tue, July 18)
T0350, T0351 (Wed, July 19)
T0325, T0352 (Thu, July 20)
T0353, T0354 (Fri, July 21)
T0355 (Sat, July 22)
T0342 (Sun, July 23)

Soft deadlines:
T0344 (Mon, July 17)
T0347 (Tue, July 18)
T0352 (Wed, July 19)
T0353-355 (Thu, July 20)
T0356 (Fri, July 21)

Thanks for reading this far :)

--
Andriy Kryshtafovych,
for CASP organizers

---

Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

All CASP7 targets have been released by now. At the moment
we have 100 "uncompromised" targets.

The facility for accepting server predictions has been shut
down. Tomorrow we are also closing the facility for accepting
server corrections.

One more target for refinement was added today - please, check
our Refinement page. We are considering a few more targets for
the refinement experiment.

It was brought to our attention that some people have misread
instructions posted at our submission page. Specifically, updating an
original prediction has been attempted by pasting into text box (1) of
the Prediction Submission Form AND specifying the PIN number of the
original prediction in field (3). We want to clarify that the PIN-number
option should only be used for making corrections to the original model
directly on the web page. We have also added a functionality to
disallow simultaneous use of any two submission options.

Targets to expire next week:
T0327 (Mon, July 24)
T0331, T0358, T0359 (Wed, July 26)
T0335, T0357 (Thu, July 27)
T0360, T0362 (Fri, July 28)
T0361, T0363 (Sat, July 29)
T0364, T0365 (Sun, July 30)

Soft deadlines:
T0357 (Wed, July 26)
T0360-362 (Thu, July 27)
T0363-365 (Fri, July 28)

--
Andriy Kryshtafovych,
for CASP organizers

---

Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

Not of much interest unless you are a participant, but for completeness! Today at 19:25.

Dear CASP7 participants,

I am writing to you from my work account as CASP account
is still unreachable.

Yesterday, starting from 3 pm we had three power disruptions at the
University. And this morning we had a big power failure at the campus
again. As a result, all our servers went down. We are working on putting
them back. So far only one server is up.

Server for accepting predictions is still down. I don't know at the
moment whether your predictions sent after 3:30pm PST yesterday reached
us or not. More on this later ...

Obviously, we will extend deadlines if we won't manage to fire up the
accepting server in the closest hour ...

--
Andriy Kryshtafovych, Ph.D.

---

Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

... and 20:23.

Dear CASP7 participants,

We have managed to bring our servers back online. I can see a huge file
(~100 MB) with the submitted predictions on the server. So there is a
big hope that all (or at least vast majority) of your predictions did
reach us but just were not processed. Hope nothing got corrupted with
our prediction accepting system and we would be able to restart it
pretty soon. Then the predictions should start flowing through our
verificators and models should start appearing in the model viewer list.
We will extend the deadline for accepting today's predictions for one
more day so that those of you who got affected would have a chance to
resubmit.

--
Andriy Kryshtafovych,
for CASP organizers

---

Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

... and 23:15.

Hi again,

Our server is currently processing the predictions that were
sent to us yesterday evening. I expect it to take several hours
to process all the backlog of predictions. Please, do not submit
copies of your predictions in the meantime. I will be monitoring
the server work and will update you on the status of prediction
acceptance in 3-4 hours. At the moment we still have >110 Mb of
predictions unprocessed.

--
Andriy Kryshtafovych,
for CASP organizers

---

Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

... 02:57. I should, perhaps, point out that the times are the times I receive the e-mail from CASP, i.e. the time here in Denmark. Danish time at the moment is summer time and thus GMT +2 hours.

At the moment, our submission server has processed the predictions sent
to us by 5:45 am PST. If you sent your prediction by that time and could
not see it in the model viewer or did not get an error message - please,
resubmit in approximately 3 hours (I estimate the backlog to be
completely dissolved by then).

Sorry for the troubles.

--
Andriy Kryshtafovych,
for CASP organizers

---

Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.